Revealing mistake: On each of Sky Captain's hangar doors, the windows are broken in the exact same places, indicating the same window rendering was simply duplicated to make the others. (00:16:45)
Continuity mistake: When the scientist is killed by the electric device in front of Totenkopf's office, he is transformed in to ashes and bones but in the following shot, there are only bones on the floor.
Continuity mistake: When Joe and Polly are running on the tree trunk, Joe loses his gun but it is a completely different one when we see it falling.
Chosen answer: About 95% is CGI. The only real part of the movie was the actors themselves (and small objects they handle), with the exception of Dr. Totenkopf, portrayed using archive footage of Laurence Olivier. Everything else was CGI.
Guy